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Say 'aaaaa' - Interactive vowel practice for second language learning
This paper reports on a system created to help language students learn the vowel inventory of Swedish. Formants are tracked, and a 3D ball moves over a vowel-chart canvas in real time. Target spheres are placed at the target values of vowels, and the students’ task is to get the target spheres. A calibration process of capturing data from three cardinal vowels is used to normalize the effects o...
full textEvidence for opposite groove-directed curvature of GGGCCC and AAAAA sequence elements.
The repetitive sequence (AGGGCCCTAGAGGGGCCC-TAG)n was previously shown to be curved by gel mobility assays. Here we show, using hydroxy radical/DNase I digestion and differential helical phasing experiments that the curvature is directed towards the major groove and is located in the GGGCCC, but not the CTAGAG segments. The effect of the GC step in the context of the GGGCCC motif is apparently ...
full textMolecular dynamics simulations and free energy calculations of netropsin and distamycin binding to an AAAAA DNA binding site
Molecular dynamics simulations have been performed on netropsin in two different charge states and on distamycin binding to the minor groove of the DNA duplex d(CGCGAAAAACGCG).d(CGCGTTTTTCGCG). The relative free energy of binding of the two non-covalently interacting ligands was calculated using the thermodynamic integration method and reflects the experimental result. From 2 ns simulations of ...
full textInduced topological changes in DNA complexes: influence of DNA sequences and small molecule structures
Heterocyclic diamidines are compounds with antiparasitic properties that target the minor groove of kinetoplast DNA. The mechanism of action of these compounds is unknown, but topological changes to DNA structures are likely to be involved. In this study, we have developed a polyacrylamide gel electrophoresis-based screening method to determine topological effects of heterocyclic diamidines on ...
full textMinimalist protein design: a beta-hairpin peptide that binds ssDNA.
A 28-residue beta-hairpin dimer (WKWK)2 with two Trp and two Lys residues on one face of each beta-sheet was shown to form a complex with single-stranded oligonucleotides at low micromolar concentrations. Each beta-hairpin of the dimer contains a cross-strand Trp-Trp pair in a diagonal orientation which has previously been shown to create a cleft for the intercalation of aromatic guests such as...
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Journal title
volume 0 issue None
pages 99- 118
publication date 2020-02
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